Abstract
BackgroundTools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.FindingsTo assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...ConclusionsThe framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.
Highlights
The diversity of tools available for visualizing and browsing genomic data has increased dramatically over the last years: Bluejay [1], GenoMap [2], GenomeComp [3], GenomeViz [4], DiProGB [5] to cite but a few
To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology
Projects aiming at supplanting or complementing current genomes browsers (GBs) are blooming as well
Summary
The diversity of tools available for visualizing and browsing genomic data has increased dramatically over the last years: Bluejay [1], GenoMap [2], GenomeComp [3], GenomeViz [4], DiProGB [5] to cite but a few. Projects aiming at supplanting or complementing current genomes browsers (GBs) are blooming as well. These different GBs provide the basic functionalities for browsing annotations on a genomic scaffold, their philosophy, functionality, interoperability and implementation are often unique or dedicated to a particular scientific context. To illustrate the use of the proposed methodology, we provide hereafter a short description of the comparison of seven GBs. Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming
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